Yes, they are both essentially the same but their movesets would be different. Big Boss would rely on CQC much more, as he excels in that catergory. Using guns would be more of a secondary for him, but still be within his moveset. Solid Snake would use guns a tad bit more, and perhaps even the Metal Gear Mk. II/III and Stealth Camoflague. Of course he would also use CQC, but to a lesser extent. With all that being said, my vote goes to Solid Snake from his MGS4 appearence. So to be more accurate, Old Snake. He narrowly beats out Big Boss, but I feel Solid Snake represents the whole Metal Gear Solid series, while Big Boss is the origin of the series.
Both are awesome but if I had a gun pointed at me I would say Big Boss. MGS 3 was the first metal gear game I ever played and it is in my top five greatest games because of the incredible story. While Solid Snake is awesome I have to go with Big Boss. Besides, the eyepatch makes him even more cool. Even cooler than the dos equis man.
BIG BOSS IS NOT SOLID SNAKE. SOLID SNAKE IS NOT A CLONE. PLAY THE WHOLE SERIES TO UNDERSTAND.
Solid Snake is a clone.